TY  - JOUR
A1  - Bordihn, Henning
A1  - Mitrana, Victor
A1  - Paun, Andrei
A1  - Paun, Mihaela
T1  - Hairpin completions and reductions
BT  - semilinearity properties
JF  - Natural computing : an innovative journal bridging biosciences and computer sciences ; an international journal
N2  - This paper is part of the investigation of some operations on words and languages with motivations coming from DNA biochemistry, namely three variants of hairpin completion and three variants of hairpin reduction. Since not all the hairpin completions or reductions of semilinear languages remain semilinear, we study sufficient conditions for semilinear languages to preserve their semilinearity property after applying the non-iterated hairpin completion or hairpin reduction. A similar approach is then applied to the iterated variants of these operations. Along these lines, we define the hairpin reduction root of a language and show that the hairpin reduction root of a semilinear language is not necessarily semilinear except the universal language. A few open problems are finally discussed.
KW  - DNA hairpin formation
KW  - Hairpin completions
KW  - Hairpin reductions
KW  - Semilinearity property
Y1  - 2020
U6  - https://doi.org/10.1007/s11047-020-09797-0
SN  - 1572-9796
VL  - 20
IS  - 2
SP  - 193
EP  - 203
PB  - Springer Science + Business Media B.V.
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Bordihn, Henning
A1  - Mitrana, Victor
A1  - Negru, Maria C.
A1  - Paun, Andrei
A1  - Paun, Mihaela
T1  - Small networks of polarized splicing processors are universal
JF  - Natural computing : an innovative journal bridging biosciences and computer sciences ; an international journal
N2  - In this paper, we consider the computational power of a new variant of networks of splicing processors in which each processor as well as the data navigating throughout the network are now considered to be polarized. While the polarization of every processor is predefined (negative, neutral, positive), the polarization of data is dynamically computed by means of a valuation mapping. Consequently, the protocol of communication is naturally defined by means of this polarization. We show that networks of polarized splicing processors (NPSP) of size 2 are computationally complete, which immediately settles the question of designing computationally complete NPSPs of minimal size. With two more nodes we can simulate every nondeterministic Turing machine without increasing the time complexity. Particularly, we prove that NPSP of size 4 can accept all languages in NP in polynomial time. Furthermore, another computational model that is universal, namely the 2-tag system, can be simulated by NPSP of size 3 preserving the time complexity. All these results can be obtained with NPSPs with valuations in the set as well. We finally show that Turing machines can simulate a variant of NPSPs and discuss the time complexity of this simulation.
KW  - Computing with DNA
KW  - Splicing
KW  - Splicing processor
KW  - Polarization
KW  - 2-tag system
KW  - Turing machine
Y1  - 2018
U6  - https://doi.org/10.1007/s11047-018-9691-0
SN  - 1567-7818
SN  - 1572-9796
VL  - 17
IS  - 4
SP  - 799
EP  - 809
PB  - Springer
CY  - Dordrecht
ER  -